Re: [AMBER] capturing free energy landscape

From: Jason Swails <>
Date: Tue, 10 Dec 2013 15:45:46 -0500

On Tue, Dec 10, 2013 at 5:23 AM, anu chandra <> wrote:

> Dear Amber users,
> I am working with all-atom MD simulations of protein-ligand system. I have
> carried out PCA analysis after 75ns of simulation. By looking at the
> collective motions along the first principle component, I could able to see
> that the protein is visiting two different conformations.Now, I am looking
> for a method to capture the free energy landscape of these conformational
> changes. If I am right, usual methodologies like meta-dynamics. AMD etc.
> are usually used to overcome the high energy barrier during the
> conformational changes. Since I could capture the conformational changes in
> my protein during the classical MD itself, it seems like the energy barrier
> is too low between these two different conformations. How can I capture
> free energy change during these conformational changes? Which method will
> be helpful for me to do this calculation?

If you have sufficient sampling without using any type of biasing
potential, you can just calculate free energies directly from the

This is typically done using a histogram along whatever reaction coordinate
you choose to define and taking the negative log of the histogram
population (divided by the population of the most populated bin if you want
to set the minimum energy to 0). Multiplied by -kT, of course...

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Dec 10 2013 - 13:00:03 PST
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